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5	5	=== **Workflow** ===
6	6
7	7	1. (((
8		-**We Use GitHub to [[Store and develop AI models, scripts, and annotation pipelines.>>https://github.com/users/manuelmenendezgonzalez/projects/1/views/1]]**
	8	+**We Use GitHub to [[Store and develop AI models, scripts, and annotation pipelines.>>https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/discussions]]**
9	9
10	10	* Create a **GitHub repository** for AI scripts and models.
11	11	* Use **GitHub Projects** to manage research milestones.
...	...	@@ -22,8 +22,92 @@
22	22
23	23	=== **1. Data Integration** ===
24	24
	25	+== Overview ==
	26	+
	27	+
	28	+Neurodiagnoses integrates clinical data via the **EBRAINS Medical Informatics Platform (MIP)**. MIP federates decentralized clinical data, allowing Neurodiagnoses to securely access and process sensitive information for AI-based diagnostics.
	29	+
	30	+== How It Works ==
	31	+
	32	+
	33	+1. (((
	34	+**Authentication & API Access:**
	35	+
	36	+* Users must have an **EBRAINS account**.
	37	+* Neurodiagnoses uses **secure API endpoints** to fetch clinical data (e.g., from the **Federation for Dementia**).
	38	+)))
	39	+1. (((
	40	+**Data Mapping & Harmonization:**
	41	+
	42	+* Retrieved data is **normalized** and converted to standard formats (.csv, .json).
	43	+* Data from **multiple sources** is harmonized to ensure consistency for AI processing.
	44	+)))
	45	+1. (((
	46	+**Security & Compliance:**
	47	+
	48	+* All data access is **logged and monitored**.
	49	+* Data remains on **MIP servers** using **federated learning techniques** when possible.
	50	+* Access is granted only after signing a **Data Usage Agreement (DUA)**.
	51	+)))
	52	+
	53	+== Implementation Steps ==
	54	+
	55	+
	56	+1. Clone the repository.
	57	+1. Configure your **EBRAINS API credentials** in mip_integration.py.
	58	+1. Run the script to **download and harmonize clinical data**.
	59	+1. Process the data for **AI model training**.
	60	+
	61	+For more detailed instructions, please refer to the **[[MIP Documentation>>url:https://mip.ebrains.eu/]]**.
	62	+
	63	+----
	64	+
	65	+= Data Processing & Integration with Clinica.Run =
	66	+
	67	+
	68	+== Overview ==
	69	+
	70	+
	71	+Neurodiagnoses now supports **Clinica.Run**, an open-source neuroimaging platform designed for **multimodal data processing and reproducible neuroscience workflows**.
	72	+
	73	+== How It Works ==
	74	+
	75	+
	76	+1. (((
	77	+**Neuroimaging Preprocessing:**
	78	+
	79	+* MRI, PET, EEG data is preprocessed using **Clinica.Run pipelines**.
	80	+* Supports **longitudinal and cross-sectional analyses**.
	81	+)))
	82	+1. (((
	83	+**Automated Biomarker Extraction:**
	84	+
	85	+* Standardized extraction of **volumetric, metabolic, and functional biomarkers**.
	86	+* Integration with machine learning models in Neurodiagnoses.
	87	+)))
	88	+1. (((
	89	+**Data Security & Compliance:**
	90	+
	91	+* Clinica.Run operates in **compliance with GDPR and HIPAA**.
	92	+* Neuroimaging data remains **within the original storage environment**.
	93	+)))
	94	+
	95	+== Implementation Steps ==
	96	+
	97	+
	98	+1. Install **Clinica.Run** dependencies.
	99	+1. Configure your **Clinica.Run pipeline** in clinica_run_config.json.
	100	+1. Run the pipeline for **preprocessing and biomarker extraction**.
	101	+1. Use processed neuroimaging data for **AI-driven diagnostics** in Neurodiagnoses.
	102	+
	103	+For further information, refer to **[[Clinica.Run Documentation>>url:https://clinica.run/]]**.
	104	+
	105	+==== ====
	106	+
25	25	==== **Data Sources** ====
26	26
	109	+[[List of potential sources of databases>>https://github.com/Fundacion-de-Neurociencias/neurodiagnoses/blob/main/data/sources/list_of_potential_databases]]
	110	+
27	27	**Biomedical Ontologies & Databases:**
28	28
29	29	* **Human Phenotype Ontology (HPO)** for symptom annotation.
...	...	@@ -184,6 +184,6 @@
184	184
185	185	=== **Why This Matters** ===
186	186
187		-* **The annotation system ensures that AI-generated insights are structured, interpretable, and clinically meaningful.**
188		-* **It enables real-time tracking of disease progression across the three diagnostic axes.**
189		-* **It facilitates integration with electronic health records and decision-support tools, improving AI adoption in clinical workflows.**
	271	+* The annotation system ensures that AI-generated insights are structured, interpretable, and clinically meaningful.
	272	+* It enables real-time tracking of disease progression across the three diagnostic axes.
	273	+* It facilitates integration with electronic health records and decision-support tools, improving AI adoption in clinical workflows.